Proteins are high value biomolecules with application in several fields, therefore the study of novel extraction methods using more biocompatible techniques is in large extent. Aqueous Biphasic Systems are increasingly being studied for that purpose, due to presenting two aqueous phases, usually protein-friendly. Fluorinated Ionic Liquids (FILs) are an emerging category of Ionic Liquids due to their unique properties, namely self-aggregation behavior, and already showing protein benign behavior. In this work, Lysozyme was used as model protein, and used to be partitioned by systems composed by IL and FIL, besides several salting-out agents, specifically inorganic salt, carbohydrates and a dihydrogen phosphate choline ([N1112OH][H2PO4]). These studies revealed favored partition to FIL-aqueous rich phase comparing with IL-rich phase. Lysozyme activity was tested for each component and after partition protocol, and maintained for most cases. Turbidimetry was used to infer the presence of some interactions between the protein and some systems elements; Tryptophan Intrinsic Fluorescence studies were carried to verify some conformation changes in the presence of IL, FIL and N1112OH][H2PO4]. Then, nano-Differential Scanning Calorimetry (nano-DSC) was used to confer the maintenance of thermal stability of Lysozyme, and determination of melting temperature (Tm). These studies have revealed the presence of some interaction between IL/FIL and protein, besides different conformational changes in Lysozyme provoked by these compounds compared to reference. Also, was observed a decrease on Tm with increasing IL and FIL concentration, however at partition conditions, FIL presented more Tm conservation than IL. This work permitted a higher insight on FIL application in ABS for protein extraction, and reveled their promising assets for this end; however more studies relatively to Lysozyme structure and thermodynamic parameters in the presence of IL/FIL are needed.